pycombat_seq: batch effect correction for RNASeq data

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.. currentmodule:: inmoose.pycombat

ComBat-Seq [Zhang2020]_ follows on the steps of ComBat, but targets specifically

RNA-Seq data. Conceptually, ComBat-Seq is based on the same mathematical

framework as ComBat, except that its replaces the normal distribution of

microarray data by a negative binomial distribution to account for the

specificities of RNA-Seq expression data.  :func:`pycombat_seq` is a direct port

of ComBat-Seq to Python. Since ComBat-Seq relies on the Bioconductor

:code:`edgeR` package, the relevant parts of :code:`edgeR` have been ported

along.  Closely following the original implementation in R, :func:`pycombat_seq`

has results very similar to those of ComBat-Seq in terms of batch effects

correction.  Additionally, :func:`pycombat_seq` is as fast, if not faster, than

the original implementation in R. It also features additional capabilities, such

as fixing a given batch as reference.

Code documentation

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.. autofunction:: pycombat_seq